I have a customer who switched from JMP Genomics to JMP Pro and is looking to replicate an analysis workflow.
Here is the description of his desired analysis:
I am trying to determine the proportion of paternal alleles in a progeny set and/or get an estimate of introgression of the male genetics to the progenies. The design consisted of a paired cross (biparental) and the other from open pollination (one female and multiple males). I remember that this can be done in JMPGenomics but cannot recall the steps. The genotype dataset has the SNP scoring system 0,1,2 (the 2 being the heterozygote).
Is this workflow possible in JMP Pro? If so, I would like to provide some general guidance on steps and platforms we would use to replicate the analysis.
Any guidance from the JMP Genomics experts would be much appreciated!
Thanks in advance,
HI @scott_allen ,
I have asked development and it looks like JMP Genomics never did this type of analysis. There is nothing specific in JMP Pro (or JMP) that would automatically do this for them. They would have to start with doing the coding/scoring themselves. Something like this.:
One would have to code alleles in the offspring with reference to the alleles in their parents, for instance, for the biparental population, allele from parent A = 0, allele from parent B=1, so an offspring in some generation after the cross of parents with both alleles from parent A would be 0+0=0, one for each parent 0+1=1, both from parent B 1+1=2. In doing this way, One can just look at the offspring and count alleles based on the 0,1,2 code.
For the open pollination, I suppose the user does not know the males, only knows the female, the code above still works, allele from female gets code 0, any other male gets code 1.
Not a great answer, but hope it offers some clarity.
